Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015045.1 Corchorus capsularis cultivar CVL-1 contig15066, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 160013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:141 original size:22 final size:23
Alignment explanation
Indices: 112--166 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
102 AAATTGAGAC
* *
112 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
133 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
155 TTTTGATAACCT
1 TTTTGATAACCT
167 CCCGATGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:368 original size:22 final size:22
Alignment explanation
Indices: 341--425 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
331 TAACTTGATT
*
341 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
*
363 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
385 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
407 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
426 TCCTCATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:438 original size:22 final size:22
Alignment explanation
Indices: 287--425 Score: 127
Period size: 22 Copynumber: 6.2 Consensus size: 22
277 TTGTGATAAT
* **
287 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
309 TAACCA-ACTTAAGAAATTTTAA
1 TAACCACAC-TATGAAATTTTGA
* ** *
331 TAACTTGATTCTATGAAATTTTGG
1 TAAC--CACACTATGAAATTTTGA
* *
355 TAACCACTCTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
* *
377 TAACTACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
399 TAACCACACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
421 TAACC
1 TAACC
426 TCCTCATGGA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
21 1 0.01
22 82 0.83
24 15 0.15
25 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:572 original size:30 final size:31
Alignment explanation
Indices: 538--596 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
528 TGGCAATTTA
*
538 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
568 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGGTACAAT
597 CAGAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:3677 original size:2 final size:2
Alignment explanation
Indices: 3670--3703 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3660 ACTAGGAAGC
*
3670 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3704 TACTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7093 original size:10 final size:11
Alignment explanation
Indices: 7069--7100 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
7059 ACACAGAATT
7069 AAAGAAAAGAA
1 AAAGAAAAGAA
7080 AAAGAAAA-AA
1 AAAGAAAAGAA
7090 AAAG-AAAGAA
1 AAAGAAAAGAA
7100 A
1 A
7101 GATTCTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.15
10 9 0.45
11 8 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:16418 original size:16 final size:16
Alignment explanation
Indices: 16397--16449 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
16387 TCATAAACAA
*
16397 TATATATTTTAATATT
1 TATATATATTAATATT
* * *
16413 TATATAAAAT-ATAAT
1 TATATATATTAATATT
16428 TATATATATTAATATT
1 TATATATATTAATATT
16444 TATATA
1 TATATA
16450 AATAAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATATTAATATT
Found at i:16425 original size:25 final size:25
Alignment explanation
Indices: 16395--16442 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
16385 AATCATAAAC
* *
16395 AATATATATTTTA-ATATTTATATAA
1 AATATA-ATTATATATATTAATATAA
16420 AATATAATTATATATATTAATAT
1 AATATAATTATATATATTAATAT
16443 TTATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATAATTATATATATTAATATAA
Found at i:16466 original size:31 final size:31
Alignment explanation
Indices: 16389--16473 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
16379 AAAAAAAATC
*
16389 ATAAACAATATATATTTTAATATTTATATAAA
1 ATAAA-AATATATATATTAATATTTATATAAA
* *
16421 ATATAATTATATATATTAATATTTATAT-AA
1 ATAAAAATATATATATTAATATTTATATAAA
*
16451 ATAAAAATATAATATAATAATAT
1 ATAAAAATAT-ATATATTAATAT
16474 AAATGAACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 10 0.22
31 32 0.70
32 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAAAATATATATATTAATATTTATATAAA
Found at i:16520 original size:11 final size:11
Alignment explanation
Indices: 16472--16537 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
16462 ATATAATAAT
*
16472 ATAAATGAAC-
1 ATAAACGAACA
* *
16482 ATAAATGAACT
1 ATAAACGAACA
*
16493 ATAAACGATCTA
1 ATAAACGAAC-A
*
16505 TTAAACGAACA
1 ATAAACGAACA
*
16516 ATAAACAAACA
1 ATAAACGAACA
*
16527 CTAAACGAACA
1 ATAAACGAACA
16538 TTAATCCAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
10 10 0.22
11 27 0.60
12 8 0.18
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.18
Consensus pattern (11 bp):
ATAAACGAACA
Found at i:26128 original size:2 final size:2
Alignment explanation
Indices: 26121--26152 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
26111 AATCCAAAGT
26121 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26153 GGTGAGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28265 original size:239 final size:239
Alignment explanation
Indices: 27836--28319 Score: 797
Period size: 239 Copynumber: 2.0 Consensus size: 239
27826 GAATCTTATT
* * *
27836 TGTATTCTCTAAGTTCCTTGTCCACAGAGAGCACACATCCATCCTCATTCACATTGGTTTGTTTA
1 TGTATTCTCTAAGTTCCTTGTCCACAGAGAGCACACATCCATCCCCATTCACATTGATTTGATTA
*
27901 CTTGTAAAGAGTCTGGAACGATAAATTCCAAGGCTCCTTTCAACAGAAAGTATACTAGTCATAGA
66 CTTGTAAAGAGTCTGGAACGATAAATTCCAAGGCTCCTTTCAACAGAAAGTATACTAATCATAGA
* * * *
27966 CCTTGCAAGGGGTAAGTAAAGCTAAGGCTCAAACATAACAAAAGCTGAATAAACAAATTCCTCTT
131 CCTTGCAAGAGGTAAGTAAAGCTAAAGCTCAAACATAACAAAAGCTCAATAAAAAAATTCCTCTT
* * * *
28031 AAAATTTTATTTTAAGGGTTAGAAAAGTTAAAATTTGTAAATGG
196 AAAATGTTATTTAAAGAGTTAAAAAAGTTAAAATTTGTAAATGG
*
28075 TGTATTCTCTGAGTTCCTTGTCCACAGAGAGCACACATCCATCCCCATTCACATTGATTTGATTA
1 TGTATTCTCTAAGTTCCTTGTCCACAGAGAGCACACATCCATCCCCATTCACATTGATTTGATTA
* * *
28140 CTTGTAAAGAGTCTGGAACGATAAATTCCAAGGCTCTTTTCAATAGAAAGTATGCTAATCATAGA
66 CTTGTAAAGAGTCTGGAACGATAAATTCCAAGGCTCCTTTCAACAGAAAGTATACTAATCATAGA
* * *
28205 CCTTGCAAGATGTAAGTAAAGCTAAAGCTCAAACATAACAAAAGTTCAATAAAAAAATTCCTTTT
131 CCTTGCAAGAGGTAAGTAAAGCTAAAGCTCAAACATAACAAAAGCTCAATAAAAAAATTCCTCTT
28270 AAAATGTTATTTAAAGAGTTAAAAAAGTTAAAATTTGTAAATGG
196 AAAATGTTATTTAAAGAGTTAAAAAAGTTAAAATTTGTAAATGG
28314 TGTATT
1 TGTATT
28320 GGGATTAGTA
Statistics
Matches: 226, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
239 226 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (239 bp):
TGTATTCTCTAAGTTCCTTGTCCACAGAGAGCACACATCCATCCCCATTCACATTGATTTGATTA
CTTGTAAAGAGTCTGGAACGATAAATTCCAAGGCTCCTTTCAACAGAAAGTATACTAATCATAGA
CCTTGCAAGAGGTAAGTAAAGCTAAAGCTCAAACATAACAAAAGCTCAATAAAAAAATTCCTCTT
AAAATGTTATTTAAAGAGTTAAAAAAGTTAAAATTTGTAAATGG
Found at i:30555 original size:30 final size:30
Alignment explanation
Indices: 30514--30571 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
30504 GCTTTTTTAT
30514 TTTGCTTTGCATTTGTTATCTCTATCCTCA
1 TTTGCTTTGCATTTGTTATCTCTATCCTCA
* *
30544 TTTGTTTTGCATTTGTTATTTCTATCCT
1 TTTGCTTTGCATTTGTTATCTCTATCCT
30572 AAAAACTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.19, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTGCTTTGCATTTGTTATCTCTATCCTCA
Found at i:32999 original size:2 final size:2
Alignment explanation
Indices: 32992--33016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32982 CACCAAGTGT
32992 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33017 GAATAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33836 original size:51 final size:51
Alignment explanation
Indices: 33777--33887 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
33767 ATATATTAGA
* * * *
33777 TCTGTTCATAACTTTTTTCA-CTGTTTATGTTTATTTTGATGTTTTTTTCAT
1 TCTGTTCATAACTTTTTTCATATGTTTATGTTTATATTGATG-TTTATACAT
***
33828 TCTGTTCATTGTTTTTTTCATATGTTTATGTTTATATTGATGTTTATACAT
1 TCTGTTCATAACTTTTTTCATATGTTTATGTTTATATTGATGTTTATACAT
33879 TCTGTTCAT
1 TCTGTTCAT
33888 TGTTTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 33 0.63
52 19 0.37
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (51 bp):
TCTGTTCATAACTTTTTTCATATGTTTATGTTTATATTGATGTTTATACAT
Found at i:33888 original size:51 final size:51
Alignment explanation
Indices: 33789--33896 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
33779 TGTTCATAAC
* * * *
33789 TTTTTTCACTGTTTATGTTTATTTTGATGTTTTTTTCATTCTGTTCATTGT
1 TTTTTTCAATGTTTATGTTTATATTGATGTTTTATACATTCTGTTCATTGT
33840 TTTTTTCATATGTTTATGTTTATATTGATG-TTTATACATTCTGTTCATTGT
1 TTTTTTCA-ATGTTTATGTTTATATTGATGTTTTATACATTCTGTTCATTGT
33891 TTTTTT
1 TTTTTT
33897 ATGTGATCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 33 0.63
52 19 0.37
ACGTcount: A:0.15, C:0.08, G:0.11, T:0.66
Consensus pattern (51 bp):
TTTTTTCAATGTTTATGTTTATATTGATGTTTTATACATTCTGTTCATTGT
Found at i:33912 original size:51 final size:52
Alignment explanation
Indices: 33803--33912 Score: 143
Period size: 51 Copynumber: 2.1 Consensus size: 52
33793 TTCACTGTTT
* * * * *
33803 ATGTTTATTTTGATGTTTTTTTCATTCTGTTCATTGTTTTTTTCATATGTTT
1 ATGTTTATATTGATGTTTTATACATTCTGTTCATTGTTTTTTTCATATGATC
*
33855 ATGTTTATATTGATG-TTTATACATTCTGTTCATTGTTTTTTT-ATGTGATC
1 ATGTTTATATTGATGTTTTATACATTCTGTTCATTGTTTTTTTCATATGATC
33905 ATGGTTTA
1 AT-GTTTA
33913 AAATTATTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 7 0.14
51 30 0.59
52 14 0.27
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (52 bp):
ATGTTTATATTGATGTTTTATACATTCTGTTCATTGTTTTTTTCATATGATC
Found at i:34824 original size:29 final size:29
Alignment explanation
Indices: 34792--34847 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
34782 TGTTAACATT
34792 TCTTT-ATGAGCAAAAAACTTTCTTTTATG
1 TCTTTCAT-AGCAAAAAACTTTCTTTTATG
* * *
34821 TCTTTCATATCTATAAACTTTCTTTTA
1 TCTTTCATAGCAAAAAACTTTCTTTTA
34848 ATGATTGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (29 bp):
TCTTTCATAGCAAAAAACTTTCTTTTATG
Found at i:41038 original size:2 final size:2
Alignment explanation
Indices: 41031--41057 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41021 TAACTATTAG
41031 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
41058 GAATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42815 original size:21 final size:21
Alignment explanation
Indices: 42791--42834 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42781 AAAAGTGTAA
42791 AAAAATAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
*
42812 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
42833 AA
1 AA
42835 TCCCAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAGC
Found at i:43104 original size:13 final size:14
Alignment explanation
Indices: 43068--43104 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
43058 TAAATGAAGT
43068 TATTTT-TTTTCCC
1 TATTTTCTTTTCCC
*
43081 T-TTTTCTTTTTCC
1 TATTTTCTTTTCCC
43094 TATTTTCTTTT
1 TATTTTCTTTT
43105 AACAAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 4 0.19
13 8 0.38
14 9 0.43
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTCTTTTCCC
Found at i:52717 original size:2 final size:2
Alignment explanation
Indices: 52710--52737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52700 TGAAAATCTC
52710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52738 CTTCATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60873 original size:51 final size:48
Alignment explanation
Indices: 60817--60916 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 48
60807 AACAAATAAC
*
60817 AAGTATGGTGCCTGATTTTAATTGAACTTGATTCACTTTTTGCTCTTGAAA
1 AAGTATGGTGCCTGATTTTAATTGAACTTGATT---TTTGTGCTCTTGAAA
*
60868 AAGTATGGTGCCTGATTTTATTTGAACTTGATTTTTGTGCTCTTGAAA
1 AAGTATGGTGCCTGATTTTAATTGAACTTGATTTTTGTGCTCTTGAAA
60916 A
1 A
60917 TAGAATATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 15 0.32
51 32 0.68
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (48 bp):
AAGTATGGTGCCTGATTTTAATTGAACTTGATTTTTGTGCTCTTGAAA
Found at i:66330 original size:26 final size:26
Alignment explanation
Indices: 66294--66357 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
66284 GACTTCTAAT
66294 TTCTTTTAATTAGTAGCAAAAAAAAG
1 TTCTTTTAATTAGTAGCAAAAAAAAG
66320 TTCTTTTAATTAGTAGCAAAAAAAAG
1 TTCTTTTAATTAGTAGCAAAAAAAAG
66346 TTCTTTTAATTA
1 TTCTTTTAATTA
66358 ATATTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (26 bp):
TTCTTTTAATTAGTAGCAAAAAAAAG
Found at i:67125 original size:19 final size:19
Alignment explanation
Indices: 67088--67127 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
67078 TTTAGAGAAG
*
67088 AATTCAAAGTGCACTAATC
1 AATTCAAAGTGCACAAATC
* *
67107 AATTCAAGGTGCAGAAATC
1 AATTCAAAGTGCACAAATC
67126 AA
1 AA
67128 AAACAATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (19 bp):
AATTCAAAGTGCACAAATC
Found at i:67399 original size:30 final size:28
Alignment explanation
Indices: 67363--67446 Score: 134
Period size: 27 Copynumber: 3.0 Consensus size: 28
67353 CATAAGCATC
*
67363 TGGTGCAGAAACTTGAACAGTAGCAGCAGG
1 TGGTGCAGAAACTTGAACAGGAGCAGC--G
67393 TGGTGCAGAAACTTGAACAGGAGCAGCG
1 TGGTGCAGAAACTTGAACAGGAGCAGCG
67421 -GGTGCAGAAACTTGAACAGGAGCAGC
1 TGGTGCAGAAACTTGAACAGGAGCAGC
67447 TGTGCGACGA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
27 26 0.49
28 1 0.02
30 26 0.49
ACGTcount: A:0.33, C:0.18, G:0.35, T:0.14
Consensus pattern (28 bp):
TGGTGCAGAAACTTGAACAGGAGCAGCG
Found at i:67973 original size:32 final size:32
Alignment explanation
Indices: 67927--67991 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
67917 TAAATTGAAA
67927 AAATATTAGATAAATAAAACAAAATAATGATG
1 AAATATTAGATAAATAAAACAAAATAATGATG
* * *
67959 AAATATTTGCTAAATAACACAAAATAATGATG
1 AAATATTAGATAAATAAAACAAAATAATGATG
67991 A
1 A
67992 TGAGTAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.26
Consensus pattern (32 bp):
AAATATTAGATAAATAAAACAAAATAATGATG
Found at i:70103 original size:14 final size:14
Alignment explanation
Indices: 70076--70114 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
70066 AATTAATACA
70076 TTAGTCTATCTTCC
1 TTAGTCTATCTTCC
* *
70090 TTAGTTTATTTTCC
1 TTAGTCTATCTTCC
*
70104 TTGGTCTATCT
1 TTAGTCTATCT
70115 CATGAATATC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.10, T:0.56
Consensus pattern (14 bp):
TTAGTCTATCTTCC
Found at i:70403 original size:23 final size:23
Alignment explanation
Indices: 70360--70404 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
70350 CAAAATCGAC
* *
70360 TCAAATTAGTCCCTAATGTCAAT
1 TCAAATCAGTCCCTAACGTCAAT
*
70383 TCAAATCAGTCCCTGACGTCAA
1 TCAAATCAGTCCCTAACGTCAA
70405 ATTGACATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (23 bp):
TCAAATCAGTCCCTAACGTCAAT
Found at i:70486 original size:31 final size:31
Alignment explanation
Indices: 70450--70552 Score: 134
Period size: 31 Copynumber: 3.3 Consensus size: 31
70440 TTAAATTGAA
70450 ATTAGGGACTGATTTGAGCCGATTTTGAAAC
1 ATTAGGGACTGATTTGAGCCGATTTTGAAAC
* *
70481 ATTAGGGATTGATTTGAGCCGATTTTGCAAC
1 ATTAGGGACTGATTTGAGCCGATTTTGAAAC
* * * * *
70512 GTTGGGGACTGATTTTAGCCGATTTTGTAAT
1 ATTAGGGACTGATTTGAGCCGATTTTGAAAC
*
70543 GTTAGGGACT
1 ATTAGGGACT
70553 TAATTAACCA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (31 bp):
ATTAGGGACTGATTTGAGCCGATTTTGAAAC
Found at i:79179 original size:32 final size:33
Alignment explanation
Indices: 79141--79229 Score: 92
Period size: 36 Copynumber: 2.6 Consensus size: 33
79131 ATAATATCAT
*
79141 AAAATCAACCTTT-A-AGAAAAAATCACATGAAA
1 AAAATCAACCTTTCATACAAAAAA-CACATGAAA
* *
79173 AAAATCAACTTTTCATACAAAGAACACATGAAAAAA
1 AAAATCAACCTTTCATACAAAAAACACATG---AAA
*
79209 AAAATCAACCTTTCTTACAAA
1 AAAATCAACCTTTCATACAAA
79230 TTAAAAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
32 12 0.26
33 7 0.15
34 6 0.13
36 22 0.47
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.21
Consensus pattern (33 bp):
AAAATCAACCTTTCATACAAAAAACACATGAAA
Found at i:90160 original size:18 final size:18
Alignment explanation
Indices: 90137--90172 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
90127 GAAACGAGAT
90137 GACTGTTGATGAGTCGGA
1 GACTGTTGATGAGTCGGA
90155 GACTGTTGATGAGTCGGA
1 GACTGTTGATGAGTCGGA
90173 TGATTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.39, T:0.28
Consensus pattern (18 bp):
GACTGTTGATGAGTCGGA
Found at i:91388 original size:34 final size:33
Alignment explanation
Indices: 91345--91423 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 33
91335 CACATCTTAT
* *
91345 TAAAATTAAGAGTTTTTTTTTTTGGCCAGAATAC
1 TAAAATTAAGAGTTTTTTCTTTTGG-CACAATAC
*
91379 TAAAATTAAGAG---TTTCTTTTGGCACACTAC
1 TAAAATTAAGAGTTTTTTCTTTTGGCACAATAC
91409 TAAAATTAAGAGTTT
1 TAAAATTAAGAGTTT
91424 AATACTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 18 0.46
31 9 0.23
34 12 0.31
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (33 bp):
TAAAATTAAGAGTTTTTTCTTTTGGCACAATAC
Found at i:125954 original size:18 final size:18
Alignment explanation
Indices: 125931--125986 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
125921 GAAACTGAAG
*
125931 ATGATTGCACGTATGATT
1 ATGATTACACGTATGATT
* *
125949 ATGATTATACGTATGACT
1 ATGATTACACGTATGATT
125967 ATGATTACACGTATGATT
1 ATGATTACACGTATGATT
125985 AT
1 AT
125987 ACGTATGACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (18 bp):
ATGATTACACGTATGATT
Found at i:126000 original size:36 final size:36
Alignment explanation
Indices: 125931--126006 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
125921 GAAACTGAAG
* *
125931 ATGATTGCACGTATGATTATGATTATACGTATGACT
1 ATGATTACACGTATGATTATGAGTATACGTATGACT
125967 ATGATTACACGTATGATTAT-ACGTATGAC-TATGACT
1 ATGATTACACGTATGATTATGA-GTAT-ACGTATGACT
126003 ATGA
1 ATGA
126007 GTAATCAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 1 0.03
36 33 0.92
37 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (36 bp):
ATGATTACACGTATGATTATGAGTATACGTATGACT
Found at i:133855 original size:13 final size:13
Alignment explanation
Indices: 133828--133866 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
133818 ACTCAACACT
133828 AATTGACTCAAAAA
1 AATTGACT-AAAAA
*
133842 AGTTGACTAAAAA
1 AATTGACTAAAAA
*
133855 AACTGACTAAAA
1 AATTGACTAAAA
133867 CCCGACAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (13 bp):
AATTGACTAAAAA
Found at i:150350 original size:12 final size:12
Alignment explanation
Indices: 150329--150373 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
150319 AGGAATAGGG
150329 AAAGATAAAGGAA
1 AAAGA-AAAGGAA
*
150342 AAGGAAAAGGAA
1 AAAGAAAAGGAA
*
150354 AAAGAAAAAGAA
1 AAAGAAAAGGAA
150366 AAACGAAA
1 AAA-GAAA
150374 TAGTGAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGGAA
Found at i:150362 original size:19 final size:19
Alignment explanation
Indices: 150335--150373 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
150325 AGGGAAAGAT
* * *
150335 AAAGGAAAAGGAAAAGGAA
1 AAAGAAAAAGAAAAACGAA
150354 AAAGAAAAAGAAAAACGAA
1 AAAGAAAAAGAAAAACGAA
150373 A
1 A
150374 TAGTGAGGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAAACGAA
Found at i:156688 original size:77 final size:73
Alignment explanation
Indices: 156537--156691 Score: 177
Period size: 77 Copynumber: 2.1 Consensus size: 73
156527 TTAACAAGGG
*
156537 GTTGGATCAAGTGGTAAGCAGTTCCAACTTAAACAGGTCTAAGGTTCGAGAACTTACATATGCAA
1 GTTGGATCAAGTGGTAAGCAGTTCCAACTTAAACAGGTCTAAGGTTCGAGAACTTACATACGCAA
*
156602 TTGTCCAT
66 CTGTCCAT
* * * * * * *
156610 GTTGGATCAAGTGGTAAGCGGCTTGTTTCAACTTAAGCAGGTCTCAGGTTCGAGACCTTGCGTAC
1 GTTGGATCAAGTGGTAA---GC-AGTTCCAACTTAAACAGGTCTAAGGTTCGAGAACTTACATAC
156675 GCAACTG-CTCAT
62 GCAACTGTC-CAT
156687 GTTGG
1 GTTGG
156692 GAGACTCACC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
73 17 0.25
76 3 0.04
77 48 0.71
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (73 bp):
GTTGGATCAAGTGGTAAGCAGTTCCAACTTAAACAGGTCTAAGGTTCGAGAACTTACATACGCAA
CTGTCCAT
Found at i:159867 original size:29 final size:27
Alignment explanation
Indices: 159825--159882 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
159815 TTTTAAGTTG
* *
159825 TTTTTTTTGGCCATCTCAAATTTTGATTA
1 TTTTTTTTGCCCA--TCAAACTTTGATTA
*
159854 TTTTTTTTTCCCATCAAACTTTGATTA
1 TTTTTTTTGCCCATCAAACTTTGATTA
159881 TT
1 TT
159883 GTTTAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 15 0.58
29 11 0.42
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (27 bp):
TTTTTTTTGCCCATCAAACTTTGATTA
Found at i:159961 original size:2 final size:2
Alignment explanation
Indices: 159954--160013 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
159944 TAAAATGGGA
159954 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
159996 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.